package jalview.json.binding.v1;

import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.HelixColourScheme;
import jalview.schemes.HydrophobicColourScheme;
import jalview.schemes.NucleotideColourScheme;
import jalview.schemes.PIDColourScheme;
import jalview.schemes.PurinePyrimidineColourScheme;
import jalview.schemes.RNAInteractionColourScheme;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TaylorColourScheme;
import jalview.schemes.TurnColourScheme;
import jalview.schemes.ZappoColourScheme;

import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;

public class AlignmentPojo
{
  private String svid = "1.0";

  private List<SequencePojo> seqs = new ArrayList<SequencePojo>();

  private List<AlignmentAnnotationPojo> alignAnnotation = new ArrayList<AlignmentAnnotationPojo>();

  private List<SequenceGrpPojo> seqGroups = new ArrayList<SequenceGrpPojo>();

  private List<SequenceFeaturesPojo> seqFeatures = new ArrayList<SequenceFeaturesPojo>();

  HashMap<String, String> appSettings = new HashMap<String, String>();

  public AlignmentPojo()
  {
  }

  public List<SequencePojo> getSeqs()
  {
    return seqs;
  }

  public void setSeqs(ArrayList<SequencePojo> seqs)
  {
    this.seqs = seqs;
  }

  public HashMap<String, String> getAppSettings()
  {
    return appSettings;
  }

  public void setAppSettings(HashMap<String, String> appSettings)
  {
    this.appSettings = appSettings;
  }

  public List<AlignmentAnnotationPojo> getAlignAnnotation()
  {
    return alignAnnotation;
  }

  public void setAlignAnnotation(
          List<AlignmentAnnotationPojo> alignAnnotation)
  {
    this.alignAnnotation = alignAnnotation;
  }

  public List<SequenceGrpPojo> getSeqGroups()
  {
    return seqGroups;
  }

  public void setSeqGroups(List<SequenceGrpPojo> seqGroups)
  {
    this.seqGroups = seqGroups;
  }

  public List<SequenceFeaturesPojo> getSeqFeatures()
  {
    return seqFeatures;
  }

  public void setSeqFeatures(List<SequenceFeaturesPojo> seqFeatures)
  {
    this.seqFeatures = seqFeatures;
  }

  public String getSvid()
  {
    return svid;
  }

  public void setGlobalColorScheme(String globalColorScheme)
  {
    for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
            .values())
    {
      if (cs.getJalviewName().equals(globalColorScheme))
      {
        // this.globalColorScheme = cs.getBioJsName();
        this.appSettings.put("globalColorScheme", cs.getBioJsName());
        break;
      }
    }
  }

  public enum JalviewBioJsColorSchemeMapper
  {
    USER_DEFINED("User Defined", "user defined", null), NONE("None", "foo",
            null), CLUSTAL("Clustal", "clustal", null), ZAPPO("Zappo",
            "zappo", new ZappoColourScheme()), TAYLOR("Taylor", "taylor",
            new TaylorColourScheme()), NUCLEOTIDE("Nucleotide",
            "nucleotide", new NucleotideColourScheme()), PURINE_PYRIMIDINE(
            "Purine/Pyrimidine", "purine",
            new PurinePyrimidineColourScheme()), HELIX_PROPENCITY(
            "Helix Propensity", "helix", new HelixColourScheme()), TURN_PROPENSITY(
            "Turn Propensity", "turn", new TurnColourScheme()), STRAND_PROPENSITY(
            "Strand Propensity", "strand", new StrandColourScheme()), BURIED_INDEX(
            "Buried Index", "buried", new BuriedColourScheme()), HYDROPHOBIC(
            "Hydrophobic", "hydro", new HydrophobicColourScheme()),

    // The color types below are not yet supported by BioJs MSA viewer
    T_COFFE_SCORES("T-Coffee Scores", "T-Coffee Scores", null), RNA_INT_TYPE(
            "RNA Interaction type", "RNA Interaction type",
            new RNAInteractionColourScheme()), BLOSUM62("Blosum62",
            "Blosum62", new Blosum62ColourScheme()), RNA_HELICES(
            "RNA Helices", "RNA Helices", null), PERCENTAGE_IDENTITY(
            "% Identity", "pid", new PIDColourScheme());

    private String jalviewName;

    private String bioJsName;

    private ColourSchemeI jvColourScheme;

    private JalviewBioJsColorSchemeMapper(String jalviewName,
            String bioJsName, ColourSchemeI jvColourScheme)
    {
      this.jalviewName = jalviewName;
      this.bioJsName = bioJsName;
      this.setJvColourScheme(jvColourScheme);
    }

    public String getJalviewName()
    {
      return jalviewName;
    }

    public String getBioJsName()
    {
      return bioJsName;
    }

    public ColourSchemeI getJvColourScheme()
    {
      return jvColourScheme;
    }

    public void setJvColourScheme(ColourSchemeI jvColourScheme)
    {
      this.jvColourScheme = jvColourScheme;
    }

  }

}